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SVA Elements Are Nonautonomous Retrotransposons that Cause Disease in Humans

2003; Elsevier BV; Volume: 73; Issue: 6 Linguagem: Inglês

10.1086/380207

1537-6605

Eric Ostertag, John L. Goodier, Yue Zhang, Haig H. Kazazian,

CRISPR and Genetic Engineering

L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements. L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements. The human genome is packed with repetitive DNA, predominantly the result of the activities of the LINE-1 (long interspersed nucleotide element–1) (or L1) retrotransposon. This retrotransposon is able to make an RNA copy of itself, then reverse transcribe the RNA into cDNA and integrate the cDNA copy into the genome. Two de novo insertions of L1 retrotransposons into the factor VIII gene of patients with hemophilia A demonstrated that they are a source of disease-causing mutation in humans (Kazazian et al. Kazazian et al., 1988Kazazian Jr, HH Wong C Youssoufian H Scott AF Phillips DG Antonarakis SE Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.Nature. 1988; 332: 164-166Crossref PubMed Scopus (598) Google Scholar; see Ostertag and Kazazian [Ostertag and Kazazian, 2001aOstertag EM Kazazian Jr, HH Biology of mammalian L1 retrotransposons.Ann Rev Genet. 2001; 35: 501-538Crossref PubMed Scopus (588) Google Scholar] for review). It was discovered subsequently that Alu elements also cause disease by inserting into genes (see Deininger and Batzer [Deininger and Batzer, 1999Deininger PL Batzer MA Alu repeats and human disease.Mol Genet Metab. 1999; 67: 183-193Crossref PubMed Scopus (678) Google Scholar] for review). Recent experimental data demonstrated that Alu elements are nonautonomous retrotransposons that use the L1 machinery for their own mobilization (Dewannieux et al. Dewannieux et al., 2003Dewannieux M Esnault C Heidmann T LINE-mediated retrotransposition of marked Alu sequences.Nat Genet. 2003; 35: 41-48Crossref PubMed Scopus (709) Google Scholar). Therefore, in addition to causing disease by retrotransposition in cis, L1 elements are also responsible for disease by mobilization of Alu elements in trans. Mobilization of short interspersed nucleotide elements (SINEs) by LINEs has also been experimentally demonstrated in other organisms (Nikaido et al. Nikaido et al., 2002Nikaido M Harada M Matsumura S Lin LK Wu Y Hasegawa M Okada N Kajikawa M LINEs mobilize SINEs in the eel through a shared 3′ sequence.J Mol Evol. 2002; 55: 284-301Crossref PubMed Scopus (56) Google Scholar). The SINE-R element was first reported as a novel retrotransposon derived from a human endogenous retrovirus, HERV-K10, and is present in the human genome at a frequency of 4,000–5,000 copies per haploid genome (Ono et al. Ono et al., 1987Ono M Kawakami M Takezawa T A novel human nonviral retroposon derived from an endogenous retrovirus.Nucleic Acids Res. 1987; 15: 8725-8737Crossref PubMed Scopus (68) Google Scholar). Ono et al. (Ono et al., 1987Ono M Kawakami M Takezawa T A novel human nonviral retroposon derived from an endogenous retrovirus.Nucleic Acids Res. 1987; 15: 8725-8737Crossref PubMed Scopus (68) Google Scholar) noted that the elements ended in an A-rich sequence and were flanked by target-site duplications (TSDs). A second group described a SINE-R sequence within the human complement C2 gene that was associated with a variable-number-of-tandem-repeats (VNTR) locus (Zhu et al. Zhu et al., 1992Zhu ZB Hsieh SL Bentley DR Campbell RD Volanakis JE A variable number of tandem repeats locus within the human complement C2 gene is associated with a retroposon derived from a human endogenous retrovirus.J Exp Med. 1992; 175: 1783-1787Crossref PubMed Scopus (46) Google Scholar). This sequence and another similar sequence from within the HLA-RP1 (STK19) gene were subsequently analyzed by a third group, who reported that the SINE-R and VNTR sequences were also associated with Alu-like sequence and occasionally were associated with hexameric repeats (Shen et al. Shen et al., 1994Shen L Wu LC Sanlioglu S Chen R Mendoza AR Dangel AW Carroll MC Zipf WB Yu CY Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region: molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication.J Biol Chem. 1994; 269: 8466-8476Abstract Full Text PDF PubMed Google Scholar). The entire structure was flanked by TSDs. Shen et al. (Shen et al., 1994Shen L Wu LC Sanlioglu S Chen R Mendoza AR Dangel AW Carroll MC Zipf WB Yu CY Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region: molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication.J Biol Chem. 1994; 269: 8466-8476Abstract Full Text PDF PubMed Google Scholar) used the term “SVA” (SINE-R, VNTR, and Alu) to describe this “composite retroposon.” Hassoun et al. (Hassoun et al., 1994Hassoun H Coetzer TL Vassiliadis JN Sahr KE Maalouf GJ Saad ST Catanzariti L Palek J A novel mobile element inserted in the alpha spectrin gene: spectrin dayton. A truncated α spectrin associated with hereditary elliptocytosis.J Clin Invest. 1994; 94: 643-648Crossref PubMed Scopus (33) Google Scholar) reported the insertion of a novel mobile element into the α-spectrin gene (SPTA1) in a recent ancestor of a family with hereditary elliptocytosis (Hassoun et al. Hassoun et al., 1994Hassoun H Coetzer TL Vassiliadis JN Sahr KE Maalouf GJ Saad ST Catanzariti L Palek J A novel mobile element inserted in the alpha spectrin gene: spectrin dayton. A truncated α spectrin associated with hereditary elliptocytosis.J Clin Invest. 1994; 94: 643-648Crossref PubMed Scopus (33) Google Scholar). We have determined that this sequence was actually the result of an SVA-mediated transduction event. We have isolated and characterized the full-length SVA precursor that created the insertion SVASPTA1. We demonstrate that SVA insertions contain the hallmarks of retrotransposition in trans by the L1 element; that is, they are flanked by L1-like TSDs, they end in a poly A tail, they can transduce 3′ sequences, and they occasionally truncate and invert during insertion. Therefore, it is highly likely that SVA elements are retrotransposed by L1 proteins acting in trans. SVA elements join Alu elements as the only active nonautonomous retrotransposons that cause disease in humans. A de novo insertion into the α-spectrin gene was caused by an SVA-mediated transduction.—We performed a BLAST search (Altschul et al. Altschul et al., 1990Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool.J Mol Biol. 1990; 215: 403-410PubMed Scopus (0) Google Scholar) of GenBank, and we were able to find the likely precursor to a previously unknown sequence inserted into the α-spectrin gene of a family with hereditary elliptocytosis (fig. 1). The BLAST search returned a nearly perfect match to a sequence contained in contig AC016142. However, the sequence of the insertion was rearranged in relation to the sequence from the contig. The 5′ end of the insertion was inverted, and there was a 22-bp deletion of the sequence at the point of inversion. This type of rearrangement is common during L1 retrotransposition (Ostertag and Kazazian Ostertag and Kazazian, 2001bOstertag EM Kazazian Jr, HH Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition.Genome Res. 2001; 11: 2059-2065Crossref PubMed Scopus (159) Google Scholar), suggesting that perhaps the inserted sequence was the result of an L1-mediated transduction (Moran et al. Moran et al., 1999Moran JV DeBerardinis RJ Kazazian Jr, HH Exon shuffling by L1 retrotransposition.Science. 1999; 283: 1530-1534Crossref PubMed Scopus (454) Google Scholar; Goodier et al. Goodier et al., 2000Goodier JL Ostertag EM Kazazian Jr, HH Transduction of 3′-flanking sequences is common in L1 retrotransposition.Hum Mol Genet. 2000; 9: 653-657Crossref PubMed Scopus (183) Google Scholar; Pickeral et al. Pickeral et al., 2000Pickeral OK Makalowski W Boguski MS Boeke JD Frequent genomic DNA transduction driven by LINE-1 retrotransposition.Genome Res. 2000; 10: 411-415Crossref PubMed Scopus (196) Google Scholar) that had inverted during the insertion process. If this hypothesis were correct, then one would predict that an active, full-length L1 element would be located 5′ from the transduced sequence. However, when we examined the 5′ sequence, we did not find a full-length L1 element; rather, we found a full-length SVA element, which suggests that the insertion into the α-spectrin gene was the result of an SVA-mediated retrotransposition event. The full-length SVA element in contig AC016142 contained evidence of a previous transduction event. In other words, the sequence that was transduced during the retrotransposition event into the α-spectrin gene was a secondary transduction event. Such composite transductions occasionally occur during L1 retrotransposition (Goodier et al. Goodier et al., 2000Goodier JL Ostertag EM Kazazian Jr, HH Transduction of 3′-flanking sequences is common in L1 retrotransposition.Hum Mol Genet. 2000; 9: 653-657Crossref PubMed Scopus (183) Google Scholar). The evidence of the original transduction was the presence of 183 bp of sequence, which we will refer to as “transduction 1,” that lay between the full-length SVA element and the secondary transduction event of 599 bp, which we will refer to as “transduction 2.” A transduced sequence acts as a molecular address that permits the identification of the precursor to the transduction event. Therefore, we performed a second BLAST search and identified the location of the first transduction. The transduction 1 sequence was an identical match to sequence from contigs AC037439 and AC068352. However, neither of these contigs contained a full-length SVA element; rather, they represented the “empty site” of this insertion (fig. 1). Structure of SVA elements.—We acquired BAC clone RP11-166N6 (accession number AC016142) (Research Genetics), isolated the full-length SVA precursor that created SVASPTA1, and cloned it into pBluescript (Stratagene) with standard molecular subcloning techniques to create pBS-SVA. We sequenced pBS-SVA using the following oligonucleotide primers: SVA5′Flank(F) (5′-CAT GGA TGG TGT CAA GCT AC-3′), SVA(Alu)R (5′-CAC CAC TGA GCA CTG AGT GAA C-3′), and T7 (5′-GTA ATA CGA CTC ACT ATA GGG C-3′). After we cloned and restriction mapped the precursor to the α-spectrin insertion, it became clear that there were errors in the assembly of contig AC016142. The GenBank sequence for contig AC016142 apparently had incorrect 5′ flanking sequence. However, this error has been corrected. From the correct sequence, we were able to surmise the structural features of a full-length SVA element (fig. 2). At their 5′ ends, full-length SVA elements have hexameric (CCCTCT) repeats. This region is followed by (1) a region containing an antisense Alu sequence, (2) a VNTR region containing multiple copies of a 35–50-bp repeat, (3) a SINE-R sequence, and (4) a polyadenylation signal and a poly A tail. The exact number of hexameric repeats present at the 5′ end of SVASPTA1 has been difficult to determine because the repeat structure is intractable to sequencing in either direction. However, from the sequencing results, we know that there are a minimum of 10 repeats. In addition, we performed a PCR across the hexamers, using primers SVA5′Flank(F) and SVA(Alu)R. From the size of this PCR product, we estimate that there are ≤13 hexameric repeats (data not shown). SVASPTA1 contains 35 repeats in the VNTR region. We aligned the repeats, using ClustalW (fig. 3A). There are two general types of VNTR, one with a range of 36–42 bp and the other with a range of 49–51 bp. We performed a cladogram on the VNTRs, using MacVector software (fig. 3B). The relationship of the VNTRs suggests that the region has expanded as the result of mispairing of the VNTR regions, followed by unequal homologous recombination. For example, the individual VNTRs from a block of six VNTRs (18–23) are most closely related to the corresponding individual VNTRs from block 24–29. One would predict that the unequal homologous recombination event that produced the duplication of the six-VNTR–block region also produced a deletion of the six VNTRs in the other SVA allele. Unequal homologous recombination has been proposed elsewhere to describe features of simple repetitive DNA elements (Levinson and Gutman Levinson and Gutman, 1987Levinson G Gutman GA Slipped-strand mispairing: a major mechanism for DNA sequence evolution.Mol Biol Evol. 1987; 4: 203-221PubMed Google Scholar). Perhaps SVA elements are hotspots for unequal homologous recombination in the human genome. Copy number and similarity.—We estimated the number of full-length and truncated SVA elements in the genome by using variable amounts of the 5′ end of the element (including as much as the first 380 bp of the Alu-like region) or the 3′ end of the element (as much as the last 380 bp of the SINE-R region) to perform BLAST searches of the draft human genome sequence in GenBank. Our BLAST searches by use of sequences from the 3′ end of SVASPTA1 suggest that there are ∼3,500–7,500 SVA sequences in the diploid human genome, which is in agreement with the estimate of the number of SINE-R sequences performed by Ono et al. (Ono et al., 1987Ono M Kawakami M Takezawa T A novel human nonviral retroposon derived from an endogenous retrovirus.Nucleic Acids Res. 1987; 15: 8725-8737Crossref PubMed Scopus (68) Google Scholar) with filter hybridization screens (Ono et al. Ono et al., 1987Ono M Kawakami M Takezawa T A novel human nonviral retroposon derived from an endogenous retrovirus.Nucleic Acids Res. 1987; 15: 8725-8737Crossref PubMed Scopus (68) Google Scholar). Estimates through use of the 5′ end of the element suggest that >2,000 of the SVA elements are full length. BLAT searches (Sugnet et al. Sugnet et al., 2002Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM Haussler D Kent WJ BLAT—the BLAST-like alignment tool.Genome Res. 2002; 12: 996-1006Crossref PubMed Scopus (5931) Google Scholar) simultaneously using both ends of the element confirmed the presence of at least several hundred full-length elements. We found many copies of SVA elements with >99% identity to recent SVA insertions in the SINE-R region, and all SVA elements were >89% identical to each other. SVA retrotransposons have evolved recently.—Retrotransposons that have been in the genome for a long time accumulate random mutations. Therefore, sequence divergence within a family of retrotransposons is correlated with the age of the retrotransposon (Boissinot et al. Boissinot et al., 2000Boissinot S Chevret P Furano AV L1 (LINE-1) retrotransposon evolution and amplification in recent human history.Mol Biol Evol. 2000; 17: 915-928Crossref PubMed Scopus (215) Google Scholar). The lack of any SVA elements with high sequence divergence probably indicates that SVAs have evolved recently. On the other hand, the low nucleotide divergence may be the result of gene conversion, which has been documented in other human retroelements (Myers et al. Myers et al., 2002Myers JS Vincent BJ Udall H Watkins WS Morrish TA Kilroy GE Swergold GD Henke J Henke L Moran JV Jorde LB Batzer MA A comprehensive analysis of recently integrated human Ta L1 elements.Am J Hum Genet. 2002; 71: 312-326Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar; Roy-Engel et al. Roy-Engel et al., 2002aRoy-Engel AM Imataka H Sonenberg N Deininger P Non-traditional Alu evolution and primate genomic diversity.J Mol Biol. 2002; 321: 423-432Crossref PubMed Scopus (53) Google Scholar). Stronger evidence for their young age comes from phylogenetic studies of the SINE-R component and its presumptive precursor, HERV-K10 (Ono et al. Ono et al., 1987Ono M Kawakami M Takezawa T A novel human nonviral retroposon derived from an endogenous retrovirus.Nucleic Acids Res. 1987; 15: 8725-8737Crossref PubMed Scopus (68) Google Scholar; Zhu et al. Zhu et al., 1992Zhu ZB Hsieh SL Bentley DR Campbell RD Volanakis JE A variable number of tandem repeats locus within the human complement C2 gene is associated with a retroposon derived from a human endogenous retrovirus.J Exp Med. 1992; 175: 1783-1787Crossref PubMed Scopus (46) Google Scholar). HERV-K10 is a retroviral-like sequence present in the genomes of humans, chimpanzees, gorillas, orangutans, and at least some Old World monkeys (Ono et al. Ono et al., 1986Ono M Yasunaga T Miyata T Ushikubo H Nucleotide sequence of human endogenous retrovirus genome related to the mouse mammary tumor virus genome.J Virol. 1986; 60: 589-598Crossref PubMed Google Scholar; Zhu et al. Zhu et al., 1994Zhu ZB Jian B Volanakis JE Ancestry of SINE-R.C2 a human-specific retroposon.Hum Genet. 1994; 93: 545-551Crossref PubMed Scopus (27) Google Scholar). One study of SINE-R sequences by Southern analysis found them present only in humans, chimpanzees, and gorillas (Zhu et al. Zhu et al., 1994Zhu ZB Jian B Volanakis JE Ancestry of SINE-R.C2 a human-specific retroposon.Hum Genet. 1994; 93: 545-551Crossref PubMed Scopus (27) Google Scholar). However, a subsequent PCR analysis of SINE-R sequences found SINE-R in all hominoid primates (Kim et al. Kim et al., 1999Kim HS Takenaka O Crow TJ Cloning and nucleotide sequence of retroposons specific to hominoid primates derived from an endogenous retrovirus (HERV-K).AIDS Res Hum Retroviruses. 1999; 15: 595-601Crossref PubMed Scopus (14) Google Scholar). Since SVA elements are all >89% similar in sequence to each other and are present only in hominoid primates, these elements are quite young by evolutionary standards, probably 200 million years have diverged to the point that they are now unrecognizable (Smit Smit, 1999Smit AF Interspersed repeats and other mementos of transposable elements in mammalian genomes.Curr Opin Genet Dev. 1999; 9: 657-663Crossref PubMed Scopus (713) Google Scholar). In addition, these elements may be valuable as markers for primate or human phylogenetic and population studies, as has been the case for the Alu element (Bamshad et al. Bamshad et al., 2003Bamshad MJ Wooding S Watkins WS Ostler CT Batzer MA Jorde LB Human population genetic structure and inference of group membership.Am J Hum Genet. 2003; 72: 578-589Abstract Full Text Full Text PDF PubMed Scopus (243) Google Scholar; Watkins et al. Watkins et al., 2003Watkins WS Rogers AR Ostler CT Wooding S Bamshad MJ Brassington A-ME Carroll ML Nguyen SV Walker JA Prasad BVR Reddy PG Das PK Batzer MA Jorde LB Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.Genome Res. 2003; 13: 1607-1618Crossref PubMed Scopus (174) Google Scholar). SVA elements are active retrotransposons.—The several thousand copies of SVA in the human genome are a relatively small number when compared with the 500,000 copies of L1 and 1,100,000 copies of Alu (Lander et al. Lander et al., 2001Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K et al.Initial sequencing and analysis of the human genome.Nature. 2001; 409: 860-921Crossref PubMed Scopus (16522) Google Scholar). There are ∼170-fold more L1 sequences and >300-fold more Alu sequences in the genome. However, this may reflect an evolutionarily young age of the SVA element rather than a lack of activity. There are several reasons to believe that SVA elements are quite active in the genome. One of the few ways to estimate retrotransposition frequency is by the number of recent or de novo disease-causing mutations that the element has caused by its retrotransposition. A recent survey of retrotransposon insertions reported 13 cases of recent or de novo disease-causing L1 insertions and 18 cases of Alu insertion (Ostertag and Kazazian Ostertag and Kazazian, 2001aOstertag EM Kazazian Jr, HH Biology of mammalian L1 retrotransposons.Ann Rev Genet. 2001; 35: 501-538Crossref PubMed Scopus (588) Google Scholar). A few additional insertions have been described in the past 2 years. In addition to the insertion into the α-spectrin gene, the SVA element has caused at least two other disease-causing insertions. A de novo SVA insertion into the BTK gene of a patient with X-linked agammaglobulinemia was reported elsewhere as a SINE-R insertion (Rohrer et al. Rohrer et al., 1999Rohrer J Minegishi Y Richter D Eguiguren J Conley ME Unusual mutations in Btk: an insertion, a duplication, an inversion, and four large deletions.Clin Immunol. 1999; 90: 28-37Crossref PubMed Scopus (49) Google Scholar). In addition, an SVA insertion into the fukutin gene is the cause of Fukuyama-type congenital muscular dystrophy in a large group of Japanese patients (Kobayashi et al. Kobayashi et al., 1998Kobayashi K Nakahori Y Miyake M Matsumura K Kondo-Iida E Nomura Y Segawa M Yoshioka M Saito K Osawa M Hamano K Sakakihara Y Nonaka I Nakagome Y Kanazawa I Nakamura Y Tokunaga K Toda T An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy.Nature. 1998; 394: 388-392Crossref PubMed Scopus (0) Google Scholar). The insertion into the fukutin gene was not a de novo event, but it is estimated to have occurred ∼102 generations ago (Colombo et al. Colombo et al., 2000Colombo R Bignamini AA Carobene A Sasaki J Tachikawa M Kobayashi K Toda T Age and origin of the FCMD 3′-untranslated-region retrotransposal insertion mutation causing Fukuyama-type congenital muscular dystrophy in the Japanese population.Hum Genet. 2000; 107: 559-567Crossref PubMed Scopus (25) Google Scholar). Therefore, despite its much lower copy number than those of L1 and Alu elements, SVA has an estimated cumulative retrotransposition activity that is only fivefold less than L1 and sevenfold less than Alu. The SVA elements in the genome have high sequence identity to each other, which suggests that they have retrotransposed recently. In addition, because the insertion in the α-spectrin gene originated from a transcript with a composite transduction, we have been able to find not only the precursor to the insertion but also the empty-site locus of the precursor to the precursor. The fact that we found the empty site suggests that the SVA element at that locus is polymorphic in the population with regard to its presence or absence. Therefore, we have evidence of multiple rounds of retrotransposition in the recent past. Other young, active retrotransposons—such as Ta-0 and Ta-1, the youngest human L1 subfamilies—also display both low sequence divergence and a high degree of polymorphism (Boissinot et al. Boissinot et al., 2000Boissinot S Chevret P Furano AV L1 (LINE-1) retrotransposon evolution and amplification in recent human history.Mol Biol Evol. 2000; 17: 915-928Crossref PubMed Scopus (215) Google Scholar; Sheen et al. Sheen et al., 2000Sheen FM Sherry ST Risch GM Robichaux M Nasidze I Stoneking M Batzer MA Swergold GD Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition.Genome Res. 2000; 10: 1496-1508Crossref PubMed Scopus (102) Google Scholar; Myers et al. Myers et al., 2002Myers JS Vincent BJ Udall H Watkins WS Morrish TA Kilroy GE Swergold GD Henke J Henke L Moran JV Jorde LB Batzer MA A comprehensive analysis of recently integrated human Ta L1 elements.Am J Hum Genet. 2002; 71: 312-326Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar; Ovchinnikov et al. Ovchinnikov et al., 2002Ovchinnikov I Rubin A Swergold GD Tracing the LINEs of human evolution.Proc Natl Acad Sci USA. 2002; 99: 10522-10527Crossref PubMed Scopus (54) Google Scholar; Brouha et al. Brouha et al., 2003Brouha B Schustak J Badge RM Lutz-Prigge S Farley AH Moran JV Kazazian Jr, HH Hot L1s account for the bulk of retrotransposition in the human population.Proc Natl Acad Sci USA. 2003; 100: 5280-5285Crossref PubMed Scopus (667) Google Scholar). A similar situation is seen among Alu elements (reviewed in Batzer and Deininger [Batzer and Deininger, 2002Batzer MA Deininger PL Alu repeats and human genomic diversity.Nat Rev Genet. 2002; 3: 370-379Crossref PubMed Scopus (988) Google Scholar]). SVA elements are nonautonomous and bear all the hallmarks of mobilization intransby the L1 retrotrans position machinery.—Many characteristics of SVA insertions are reminiscent of L1 insertions. First, some insertions are 5′ truncated (e.g., the BTK insertion), and others are both 5′ truncated and inverted (e.g., the α-spectrin insertion). These are both common processes during L1 retrotransposition. Second, they end in a poly A tail directly following a poly A signal. This may indicate that the adenine bases between the poly A signal and the cleavage site have been positively selected for by L1 target-primed reverse transcription (TPRT), the process that L1 elements are thought to use when integrating into the genome (Luan et al. Luan et al., 1993Luan DD Korman MH Jakubczak JL Eickbush TH Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition.Cell. 1993; 72: 595-605Abstract Full Text PDF PubMed Scopus (864) Google Scholar). Third, they occasionally bypass their own poly A signal in favor of a downstream signal, which results in a transduction event. Therefore, their retrotransposition does not depend on any specific 3′ sequence. The lack of any 3′ sequence requirements, other than a poly A tail, for retrotransposition is consistent with L1 TPRT. Last, they are flanked by 10-20-bp long TSDs, and the sequences of predicted cleavage sites are the same as those of the L1 endonuclease, which is 3′-AA/TTTT-5′ and minor variations (Feng et al. Feng et al., 1996Feng Q Moran JV Kazazian Jr, HH Boeke JD Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition.Cell. 1996; 87: 905-916Abstract Full Text Full Text PDF PubMed Scopus (808) Google Scholar; Jurka et al. Jurka, 1997Jurka J Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons.Proc Natl Acad Sci USA. 1997; 94: 1872-1877Crossref PubMed Scopus (410) Google Scholar). For example, the predicted cleavage site of the α-spectrin insertion is 3′-TA/TTCT-5′, and that of the SVASPTA1 is 3′-AA/TTTT-5′. These data are a strong indication that the L1 retrotransposition machinery mediates their retrotransposition. Minimum sequence requirements of a human nonautonomous retrotransposon.—A nonautonomous retrotransposon depends on the retrotransposition machinery of an autonomous retrotransposon to propagate itself. L1 is the only active retrotransposon in the human genome. Therefore, any human nonautonomous element must contain the sequence requirements that would allow it to be retrotransposed by L1. One obvious requirement is an internal promoter that permits expression in the same tissue and at the same time as L1 retrotransposition is occurring. The L1 element has a germline-specific promoter and is able to retrotranspose in the germline (Ostertag et al. Ostertag et al., 2002Ostertag EM DeBerardinis RJ Goodier JL Zhang Y Yang N Gerton GL Kazazian Jr, HH A mouse model of human L1 retrotransposition.Nat Genet. 2002; 32: 655-660Crossref PubMed Scopus (157) Google Scholar). Presumably, the SVA promoter also expresses in the human germline. A nonautonomous element must also have any sequences required for transcription located downstream of the transcription initiation site; otherwise, they would be lost on retrotransposition. Full-length SVA elements in the genome tend to begin within the hexameric region, suggesting that transcription is directed to initiate within this region. Further, a human nonautonomous retrotransposon must have the ability to be reinserted into the genome by the L1 TPRT mechanism. Apparently, the only absolute sequence requirement for L1-mediated TPRT is the presence of a poly A tail (Roy-Engel et al. Roy-Engel et al., 2002bRoy-Engel AM Salem A-H Oyeniran OO Deininger L Hedges DJ Kilroy GE Batzer MA Deininger PL Active Alu element “A-tails”: size does matter.Genome Res. 2002; 12: 1333-1344Crossref PubMed Scopus (105) Google Scholarb; Dewannieux et al. Dewannieux et al., 2003Dewannieux M Esnault C Heidmann T LINE-mediated retrotransposition of marked Alu sequences.Nat Genet. 2003; 35: 41-48Crossref PubMed Scopus (709) Google Scholar). SVA elements contain a poly A tail that is very similar to that of L1. There may be an additional requirement of a human nonautonomous retrotransposon. The only nonautonomous retrotransposons in the genome with evidence of current activity are the Alu elements and the SVA elements. It would seem that there is something special about Alu transcripts and SVA transcripts that allows them to retrotranspose at such high frequencies, when almost all other transcripts are not trans complemented at appreciable levels (Wei et al. Wei et al., 2001Wei W Gilbert N Ooi SL Lawler JF Ostertag EM Kazazian HH Boeke JD Moran JV Human L1 retrotransposition: cis-preference vs. trans-complementation.Mol Cell Biol. 2001; 21: 1429-1439Crossref PubMed Scopus (439) Google Scholar), including those that are more highly expressed in the germline. It is interesting that Alus and SVAs both have Alu sequence components. Perhaps the Alu sequences are important in the trans complementation by L1, placing the element RNA in close proximity to the L1 RNA, either on the ribosome or within a ribonucleoprotein particle (Boeke Boeke, 1997Boeke JD LINEs and Alus—the polyA connection.Nat Genet. 1997; 16: 6-7Crossref PubMed Scopus (198) Google Scholar). H.H.K. was supported by a National Institutes of Health grant. E.M.O. was supported by a Howard Hughes Medical Institute predoctoral fellowship.